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Table 3 BLAST parameters and options

From: Having a BLAST with bioinformatics (and avoiding BLASTphemy)

Parameter Use Parameter type Default setting
(a) Parameters mentioned in the text and Box 2
   -M Matrix String BLOSUM62
   -r Reward for a nucleotide match (BLASTNonly) Integer 1
   -q Penalty for a nucleotide mismatch (BLASTNonly) Integer -3
   -G Cost to open a gap (zero invokes default behavior) Integer 0
   -E Cost to extend a gap (zero invokes default behavior) Integer 0
   -F Filter query sequence String T
   -W Word size; default length is used if set to zero Integer 0
   -z Effective length of the database (use zero to get the real size) Real 0
   -e Expectation value (E) Real 10.0
(b) Additional useful parameters
   -i Name of the query file Filename "stdin"
   -m Alignment viewing options, which include:   
     0 Pairwise alignment   
     1 Query-anchored showing identities   
     2 Query-anchored, no identities   
     7 XML output Integer 0
   -o Name of the BLAST report output file Filename "stdout"
   -f Threshold for extending hits; default is used if set to zero Integer 0
   -g Perform gapped alignment (not available with TBLASTX) T/F T
   -Y Effective length of the search space (use zero get the real size) Real 0
   -S Query strands to search against the database (for BLAST [NX], and TBLASTX) 3 is both, 1 is top, 2 is bottom Integer 3
   -T Produce HTML output T/F F
   -y Drop-off (X) for BLAST extensions, in bits (0.0 invokes default behavior) Real 0.0
   -Z X drop-off value for final gapped alignment (in bits) Integer 0
  1. Parameters are preceded by a dash when used with the stand-alone version of BLAST; the web interfaces uses boxes and drop-down menus to control many of the same parameters. Parameters are given in the table in the order that they are mentioned in the text or on using NCBI-BLAST; additional parameters are listed at the NCBI [38]. Abbreviations: T/F, true or false; for BLAST variants see Table 1. 'Query-anchored' means that the query string is used as the 'top line' of the alignment.